Just posted this in another thread too:
I have a civic 97 Vti and i had the same problem. After many mechanics, i decided to tune it up myself
What my basic engineering skills say to me "The air mixture during idle is too lean, that why when i depress the pedal, the RPM goes down very low. Of course it should make sense, the ECM is not controlling the mixture settings for CNG and because the engine is 1.6, it 'should' need a richer mixture". So what i did was...gave the CNG mixture screw about 1.5-2 turn counter-clockwise.
The result: more stable RPM at idle, better acceleration, lower gas economy (with mixture settings done by enercon, i had 110 km/55kg cyl...now i have like 90-100) . If you dont care about such a small difference in economy, then i would suggest you play with the GAS mixture screw thingi.
Also...i once also remove the air blockage (near the air filter) that is done for CNG. The result was that RPM on idle almost got as good as petrol. The downside was that i had to increase the mixture so much that economy went down to as low as 60-80km.
Also, stop getting the throttle body cleaned. Most mechanics are just eager to open it up...but honestly, it doesn't get bogged up that fast. The problem with RPM is mainly because:
The mixture is too lean
The spark is not so good (and yes i heard all over the net that bosch 4 tips are a strict NO for Hondas, so if you have NGK plugs, stick with them. The wires usually dont get bad so soon, but do check them. Start the engine in full darkness and try to notice if you see some spark leaking out from the wires. People use water on the wire to see it, but i wont recommend it somehow )
The IAC is not behaving correctly (which i doubt. It at the back of the throttle body, get it open and fill it up with some good throttle body cleaner and rinse after 2-3 minutes and dry it with a blower, thats it)
The AC condenser fan is not fast enough. (Yes that happened to me. The AC would trip too much and idle is really low when AC is turned on. Ask some AC mechanic if the condenser fan is fast enough)
I also rotated the distributor just slightly to advance the timing a bit more (Wont recommend it though, the difference is very slight because the CNG people already do that on installation)
Other then that i don't really think there can be any thing wrong. Also my car is MT and i gather your's is AT, so maybe other thing can be wrong.
Also if anyone feels my "engineering" is not so correct, please do let me know. Good luck with getting the idle problem fixed.